Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate HSERO_RS20315 HSERO_RS20315 imidazole glycerol phosphate synthase
Query= curated2:Q3Z6V7 (237 letters) >FitnessBrowser__HerbieS:HSERO_RS20315 Length = 254 Score = 135 bits (341), Expect = 6e-37 Identities = 83/225 (36%), Positives = 127/225 (56%), Gaps = 16/225 (7%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GR V+ G E + DPV A R+ GA L +D+ ++DG + Sbjct: 7 IIPCLDVTAGRVVK---GVNFLELRDAGDPVEIARRYDEQGADELTFLDITASSDGRDLI 63 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 ++I +A+ IP+ VGGG+R+++ V++LL AG D+V + T AV NP+LV + ++Y + Sbjct: 64 LDIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKVGINTSAVTNPQLVADAASKYGS 123 Query: 122 DSVAVSIDARNG-----KVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDGTLSE 176 + V+IDA+ +V T G +T +DA+E AR M +LG + T + RDGT S Sbjct: 124 QCIVVAIDAKRAGDGKWEVYTHGGRKATGLDAVEWARKMAQLGAGEILLTSMDRDGTKSG 183 Query: 177 PNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDIGAEGAIVGKA 221 + R + A+++PVIASGGV L L A+G GKA Sbjct: 184 FDLDLTRAVSEAVSIPVIASGGVGGLQDL-------ADGITKGKA 221 Score = 31.6 bits (70), Expect = 2e-05 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 1/93 (1%) Query: 31 DPVGTAMRWQSLGAPRLHVVDLDGAADGESVNFELIREIANSALIPVEVGGGIRSMDTVK 90 D V A + LGA + + +D + +L R ++ + IPV GG+ + + Sbjct: 154 DAVEWARKMAQLGAGEILLTSMDRDGTKSGFDLDLTRAVSEAVSIPVIASGGVGGLQDLA 213 Query: 91 KLLTAG-VDRVILGTVAVENPELVREICARYAD 122 +T G D V+ ++ V+E AD Sbjct: 214 DGITKGKADAVLAASIFHYGQHTVQEAKRFMAD 246 Lambda K H 0.318 0.136 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 177 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 237 Length of database: 254 Length adjustment: 24 Effective length of query: 213 Effective length of database: 230 Effective search space: 48990 Effective search space used: 48990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory